You can have team-based or private repos hosted by Keybase. Everything is encrypted and signed before it leaves your computer, and decrypted and verified when your computer downloads it. But your local checkout of that git repo is unencrypted. It's just a normal repo. So Github Desktop has full access to it, like it does for all files in your local filesystem.

Git repository are private for you or for a team that you select.

Yes, everything is encrypted on your machine locally.

From what I understood (I haven't actually used the product), the repository is in the decrypted state on your local machine and is fully encrypted while being stored on the remote.

re: #1 I just tried it - they are giving you an encrypted git remote. So you create a new repo with them, then you can clone it somewhere (or add it as a remote) and push to it.